Description Usage Arguments Details Value Author(s) Examples

Fit logistic regression via Generalized Estimation Equation (GEE) to test gene-environment or gene-gene interactions between a dichotomous phenotype
and all imputed SNPs in a genotype file in family data under additive genetic model. The interaction term is the product of SNP genotype and a covariate for interaction (`cov.int`

).
The covariate for interaction (`cov.int`

) can be SNP genotype (gene-gene interaction) or an environmental factor (gene-environment interaction). Only one
interaction term is allowed. When `cov.int`

is dichotomous, stratified analyses can be requested by specifying `sub`

="Y". The covariance between the main
effect (SNP) and the interaction effect is provided in the output when stratified analysis is not requested. Each family is treated as
a cluster, with independence working correlation matrix used in the robust variance estimator.
This function applies the same interaction test to all SNPs in the imputed genotype data.
The interaction test is carried out by `geepack.lgst.int.imputed`

function from `GWAF`

where the
the `geese`

function from package `geepack`

is used.

1 2 | ```
geepack.lgst.int.batch.imputed(genfile,phenfile,pedfile,outfile,phen,
covars,cov.int,sub="N",col.names=T,sep.ped=",",sep.phe=",",sep.gen=",")
``` |

`genfile` |
a character string naming the genotype file for reading (see format requirement in details) |

`phenfile` |
a character string naming the phenotype file for reading (see format requirement in details) |

`pedfile` |
a character string naming the pedigree file for reading (see format requirement in details) |

`outfile` |
a character string naming the result file for writing |

`phen` |
a character string for a phenotype name in |

`covars` |
a character vector for covariates in |

`cov.int` |
a character string naming the covariate for interaction, the covariate has to be included in |

`sub` |
"N" (default) for no stratified analysis, and "Y" for requesting stratified analyses (only when |

`col.names` |
a logical value indicating whether the output file should contain column names |

`sep.ped` |
the field separator character for pedigree file |

`sep.phe` |
the field separator character for phenotype file |

`sep.gen` |
the field separator character for genotype file |

Similar to the details for `geepack.lgst.int.batch`

but here the SNP data contains imputed genotypes (allele dosages)
that are continuous and range from 0 to 2.

No value is returned. Instead, results are written to `outfile`

.
If stratified analyses are requested, the result file will include the following columns. Otherwise, `cov_beta_snp_beta_int`

will be included instead of
the results from stratified analyses, that is, `beta_snp_cov0`

, `se_snp_cov0`

, `pval_snp_cov0`

, `beta_snp_cov1`

, `se_snp_cov1`

,
and `pval_snp_cov1`

.

`phen ` |
phenotype name |

`snp ` |
SNP name |

`covar_int ` |
the covariate for interaction |

`n ` |
sample size used in analysis |

`AF ` |
allele frequency of the coded allele |

`nd ` |
the number of individuals in affected sample |

`AFd ` |
allele frequency of the coded allele in affected sample |

`model ` |
genetic model used in analysis, additive model only |

`beta_snp ` |
regression coefficient of SNP covariate |

`se_snp ` |
standard error of |

`pval_snp ` |
p-value of testing |

`beta_snp_cov0 ` |
regression coefficient of SNP covariate in stratified analysis using the subset where |

`se_snp_cov0 ` |
standard error of |

`pval_snp_cov0 ` |
p-value of testing |

`beta_snp_cov1 ` |
regression coefficient of SNP covariate in stratified analysis using the subset where |

`se_snp_cov1 ` |
standard error of |

`pval_snp_cov1 ` |
p-value of testing |

`beta_int ` |
regression coefficient of the interaction term |

`se_int ` |
standard error of |

`pval_int ` |
p-value of testing |

`remark ` |
warning or additional information for the analysis, 'not converged' indicates the GEE analysis did not converge; 'logistic reg' indicates GEE model is replaced by logistic regression; 'exp count<5' indicates any expected count is less than 5 in phenotype-genotype table; 'not converged and exp count<5', 'logistic reg & exp count<5' are noted similarly; 'collinearity' indicates collinearity exists between SNP and some covariates |

Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>

1 2 3 4 5 6 | ```
## Not run:
geepack.lgst.int.batch.imputed(phenfile="simphen.csv",genfile="simgen.csv",
pedfile="simped.csv",phen="CVD",outfile="simout.csv",covars=c("sex","age"),cov.int="sex",
sub="Y",sep.ped=",",sep.phe=",",sep.gen=",")
## End(Not run)
``` |

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